Merge branch 'release/v3.1.0'

cancerit · Jul 24, 2017 · 0eae290 · 0eae290
2 parents 0216f43 + 9877458
commit 0eae290
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Showing 6 changed files with 27 additions and 8 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -32,7 +32,7 @@ script:
  - cd cgpBigWig
  - ./setup.sh $HOME/PCAP-opt
  - cd ../
- - git clone --depth 1 --single-branch --branch dev https://github.com/ICGC-TCGA-PanCancer/PCAP-core.git
+ - git clone --depth 1 --single-branch --branch develop https://github.com/cancerit/PCAP-core.git
  - cd PCAP-core
  - ./setup.sh $HOME/PCAP-opt
  - cd ../

diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,7 @@
+### 3.1.0
+* Use newer alleleCount that includes faster 'dense snps' option
+* Minor modification to README.md layout
+
 ### 3.0.2
 * Moved call to create 1000genome loci filename hash to before use of threads to avoid glob bug in perl 5.16.3
 

diff --git a/README.md b/README.md
@@ -3,8 +3,9 @@ cgpBattenberg
 
 An installation helper, perl wrapper and the R program Battenberg which detects subclonality and copy number in matched NGS data.
 
-[![Build Status](https://travis-ci.org/cancerit/cgpBattenberg.svg?branch=master)](https://travis-ci.org/cancerit/cgpBattenberg) : master
-[![Build Status](https://travis-ci.org/cancerit/cgpBattenberg.svg?branch=dev)](https://travis-ci.org/cancerit/cgpBattenberg) : dev
+| Master | Dev |
+|---|---|
+| [![Build Status](https://travis-ci.org/cancerit/cgpBattenberg.svg?branch=master)](https://travis-ci.org/cancerit/cgpBattenberg) | [![Build Status](https://travis-ci.org/cancerit/cgpBattenberg.svg?branch=dev)](https://travis-ci.org/cancerit/cgpBattenberg) |
 
 ## Installation
 

diff --git a/perl/lib/Sanger/CGP/Battenberg.pm b/perl/lib/Sanger/CGP/Battenberg.pm
@@ -25,7 +25,7 @@ use strict;
 
 use Const::Fast qw(const);
 use base 'Exporter';
-our $VERSION = '3.0.2';
+our $VERSION = '3.1.0';
 our @EXPORT = qw($VERSION);
 
 1;

diff --git a/perl/lib/Sanger/CGP/Battenberg/Implement.pm b/perl/lib/Sanger/CGP/Battenberg/Implement.pm
@@ -51,7 +51,7 @@ use PCAP::Bam;
 
 use Data::Dumper;
 
-const my $ALLELE_COUNT_CMD => q{ -l %s -b %s -o %s -m %d -r %s};
+const my $ALLELE_COUNT_CMD => q{ -l %s -b %s -o %s -m %d -r %s -d};
 const my $RUN_FUNC => q{ -e '%s %s'};
 const my $SOURCE => q{source("%s"); };
 const my $LIBRARY => q{library(Battenberg);};

diff --git a/setup.sh b/setup.sh
@@ -21,6 +21,12 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 ########## LICENCE ##########
 
+EXP_ACV="3.3.0"
+
+version_gt () {
+  test $(printf '%s\n' $@ | sort -V | head -n 1) == "$1";
+}
+
 if [[ ($# -ne 1 && $# -ne 2) ]] ; then
   echo "Please provide an installation path such as /opt/pancan and optionally perl lib paths to allow, e.g."
   echo "  ./setup.sh /opt/myBundle"
@@ -88,23 +94,31 @@ set +e
 PCAP=`perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' PCAP`
 if [[ "x$PCAP" == "x" ]] ; then
   echo "PREREQUISITE: Please install PCAP-core (v1.12+) before proceeding:"
-  echo "  https://github.com/ICGC-TCGA-PanCancer/PCAP-core/releases"
+  echo "  https://github.com/cancerit/PCAP-core/releases"
   exit 1;
 else
   # need the leading 'v' on versions so comparison of those that don't have hotfix element behave correctly, i.e. (X.X, rather than X.X.X)
   GOOD_VER=`perl -Mversion -e "version->parse(q{v$PCAP}) >= version->parse(q{v}.q{1.12}) ? print qq{1\n} : print qq{0\n};"`
   if [ $GOOD_VER -ne 1 ]; then
     echo "PREREQUISITE: Please install PCAP-core (v1.12+) before proceeding (version too old):"
-    echo "  https://github.com/ICGC-TCGA-PanCancer/PCAP-core/releases"
+    echo "  https://github.com/cancerit/PCAP-core/releases"
     exit 1;
   fi
 fi
 
 AC=`perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' Sanger::CGP::AlleleCount`
 if [[ "x$AC" == "x" ]] ; then
-  echo "PREREQUISITE: Please install alleleCount before proceeding:"
+  echo "PREREQUISITE: Please install alleleCount version >= $EXP_ACV before proceeding:"
   echo "  https://github.com/cancerit/alleleCount/releases"
   exit 1;
+else
+  if version_gt $AC $EXP_ACV; then
+    echo "  alleleCounter version is good ($AC)"
+  else
+    echo "PREREQUISITE: Please install alleleCount version >= $EXP_ACV before proceeding (Found version $AC):"
+    echo "  https://github.com/cancerit/alleleCount/releases"
+    exit 1;
+  fi
 fi
 
 VCF=`perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' Sanger::CGP::Vcf`